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Jim Pipas writes:
1. Geographic Breakdown. The data can be broken down by location if you download Table S2. It is in the last column. We didn't discuss the data by location because for this paper we took a single sample from each site. Thus, this is a snapshot of viral diversity at the moment the sample was taken. As we indicate in Equation 1, the probability of detecting a given virus is dictated by a number of time-dependent variables. For example, climate or time of the season might be expected to impact the number of a specific type of virus present. We felt that to make conclusions about location we would need to collect many more samples under a number of different conditions. We are doing this now.
2. I am not sure why we didn't see any negative strand RNA viruses or poliovirus. There are three possibilities that we are testing. One is that the method of virion enrichment, in this case flocculation, did not capture these particular viruses. The second is that they are present below our limits of detection. That is, we need to sequence deeper. We know that there are viruses present in the samples (detected by PCR) that we do not detect by sequencing. The final formal possibility is that these viruses are not present in our samples. I will let you know what we find.
3. How many species of hosts? The number 1.8 million does include bacteria but clearly this is a serious underestimate. I too have seen that this number is likely to be revised to 8 million but I have not seen this estimate published in a scientific journal yet. We decided to go with the published number. I agree with you that there are many many more bacterial species that await discovery, and that means many many many more viruses.
In TWiV 151 at about 54:40 Alan says that "the general lifestyle of macrophages, which do kinda make a living this way, they go around eating stuff thats not supposed to be in the blood stream". I couldn't help but to catch this error.
Alan, it was my understanding (from my basic Immunology course) that Macrophages are monocytes while in circulation, and it is not until they have left the bloodstream into tissue that they mature into macrophages.
P.S. Alan I greatly enjoy your input as a writer!
Hello Gentlemen (and Alan),
I wanted to bring to your attention the NUMEROUS dangers of "pitches" or fields, especially ones that aren't as well kept as the professionals'...
My fiance plays rugby. The field is not only home to rugby games but it serves as a temporary home to plenty of wildlife. By wildlife, I mean Canada geese. The field sees many flocks of geese who are not "potty trained". The public also allows their canine companions to run and excrete on the field. One home game last fall after extensive rain, the field was very soft. Unfortunately, the field has a hidden slab of concrete about 4 inches below the surface. My fiance launched himself to tackle his opponent and his knee sank more than 4 inches right at the corner of that concrete slab... Sparing the gory details (and the video, I just included a gory still), he was taken by ambulance to hospital where the emergency department decided the wound was too deep to be cleaned while he was conscious.
The Dr. that performed his initial surgery cultured the wound and gave him IV antibiotics overnight. The laceration was stapled completely shut (no drain was placed) and the bandage was instructed to be removed in 5 days, no sooner.
When the bandages were removed the area was swollen, tender, and red coloration extended up his thigh almost to his groin. By the next day my fiance had a high fever and went to the doctor's office where the original doctor's partner sent him immediately back to the hospital.
The original cultures were never finished. Secondary cultures showed gram positive and gram negative bacteria and the majority of what was cultured came from "fecal material". The IV antibiotics were not enough to knock out the infection. He was subjected to 4 more surgeries, lost part of his patella, and stayed another 10 days in the hospital. He will never be without pain in that knee again.... Not because of the accident on the field, but because of the secondary infection.
I know this would be more appropriate for TWIM but I wanted to let the TWIV team know what dangers are on our fields.
Thanks! Hope I don't gross you out with the pictures. Let me know if you want the video of them cleaning it out with just sub-q analgesics!
Dear Vince, Rich and virology podcasters, thanks for the great podcasts! I am a beginner in the world of science, biology, and dare I say virology. I returned to school two years ago as a 38 year old truck driver, and am seeking a bachelors in science. I would like to enter the medical field in some way, and find your podcasts to be highly stimulating. I have been listening to your virology podcast in addition to your virology class lectures from Columbia for about a year now and find it increasingly interesting. I find it takes me about 4 times per lecture to actually grasp a lot of the info, but I am not giving up. One of the first things I learned was that for a virus to be successful it needs three important parts, entry into a host cell, replication, and it needs release out of the cell. Recently I read information on how the influenza virus can be affected by drugs which can indirectly inhibit the release of new virus particles and I have a couple questions, I am interested to know more about the effects of the antiviral medications amantadine and rimantadine on reducing the severity of the influenza virus. Do these drugs actually stabilize the bodies PH? and if so, how far does the PH have to shift before the virion will release its contents into the cytosol of a host cell? There are also the drugs oseltamivir and zanamavir which effect both A and B types of influenza by blocking the glycoprotein neuraminidase so the new virus particles can not be released. How well do these drugs work? And if they do, why are they not more well known?
Thanks, virology want-to-be
You're probably bored with hearing this by now, but you guys are great! Congratulations on the great job of making virology accessible to the masses. We are not as dumb as television and the newspapers would lead you to believe.
I've been listening since just after you started podcasting, and I've been meaning to email you for about two years. I've got a lot of question saved up - feel free to stop reading at any point...
1) A few episodes ago, a listener asked for suggestions for virology software. My suggestions is a pc game style virtual virology lab, where you could grow virtual viruses in a virtual culture medium containing virtual cells. The cells may or may not have the correct receptors on their surface to allow the virus to enter, and even then, they may not be able to replicate. You could find this out by doing virtual plaque assays - all this with no undergraduates spilling anything, or catching anything. The virtual virus would mutate at each replication cycle - maybe enhancing its virulence or transmissibility.
2) Last year some time, you reviewed a paper regarding replication of viruses which had been tagged with different coloured fluorescent protein. When they infected cells at quite high moi, there were few progeny expressing mixtures of colours - most expressed single colours. I didn't really understand the significance of this at the time. Is it just saying a cell is not just a bag of chemicals, but has a very structured interior? Is is saying more than that?
3) For us non academics, I'd love to hear a "day in the life" episode of a graduate student, a post doc, a PI … and so on.
4) Being an Australian, I'm always interested in your discussions of myxomatosis, calcicvirus, henrda and dengue. Alan's prescription "don't raise horses in the rainforest" is a little hard to follow - there are large flying fox colonies in the botanical gardens of both Melbourne and Sydney - luckily there are no inner city horses! Here's a link http://www.csiro.au/science/Myxomatosis-History.html to a myxomatosis story - read the paragraph headed "Hype lead to panic" - there are some famous names in it. My mother told me she had dengue several times as a child, growing up in Queensland, and was really ill.
I'm working my way through Vince's online virology course - it has really helped me understand the podcasts. (Like Dixon, I now know there are seven fundamental types of viruses).
PS. Here a a couple more things I almost forgot. I'd really like to hear more about the fossil viruses in the human genome. You had a great episode on that quite a while ago, and it left me wanting more. Also, I'd like to hear about the process of getting a vaccine out of the lab and ready for release. You've touched on if briefly several times. I had no idea it was such a large undertaking - more details, please...